Well, I think my problem is two fold.
Here is my procedure for squaring up a board.
First, I run the rough edge on the jointer to get something fairly straight. Then I take it to the table saw and rip a good edge, using the just jointed edge against the fence. Run that edge on the jointer and then use that good edge to rip the board to size. I know it's a lot of extra steps, but I have had no luck squaring up a 4' board on this jointer.
In the process of this, I happened to put a straight edge on the fresh cut from the table saw, and lo and behold, it was bowed. After a little more looking, it turns out my fence is bowed. It must only show up on the longer boards, cause I never noticed it before.
I put a straight board on the fence and followed the same procedure and got good edges on 7 of the 8 boards. I'd guess the 8th was pilot error.
I know the jointer is too small to effectively square a board that long, but unfortunately thats all I have for now.
I'll keep the suggestions in mind, and see about the height of the knives.